After heeding Maria's plea and defeating the Artificial Chaos at Lost Impact, or beating Sonic the Hedgehog in a race for the cyan Chaos Emerald in Space Gadget, Shadow and Sonic are aboard The ARK, and Sonic spots the Black Comet. Sonic fills in Shadow on what the Black Comet is and wonders if the Black Creatures are somehow related to the Comet. Shadow senses the presence of aliens aboard the Comet and then Sonic and Shadow race to the Comet. Shadow and Sonic apparently used Tails' shuttle to fly across. Once aboard, the player can choose to either help Sonic find Black Doom at the core of the comet; as they follow his giant holographic broadcasts to hunt the alien prophet down, or aid Doom's Eye to fulfill a different mission - activate all four defensive shields to secure the Comet against G.U.N.'s counterattack.
Located behind the second checkpoint on the bottom level. It is contained within a cage that is guarded by two Black Assassins that must be defeated in order to claim the key.
Pass through the large loop after the third checkpoint. When you reach the room with the Black oaks, go up the right ramp and destroy the rock to reveal the key.
Don't activate the second Shield! just continue forward, the key is located in the back of that room to the right in a secret area.
Activate the second shield when you reach the area with the large craft and the black arms cannon. Then, look to your left.
Just after the secret door, Light Dash up to the next area, and ride the platform to the path on the other side with the key.
Activate all the Black Comet's shields!
Activate the four shields.
A shield is activated when it is attacked and the red ball is on top.
In this level there are quite a few secret doors however, behind all the doors are the same objects: mounted cannon turrets.
This is only stage where you don't need a time bonus to get an A rank for the Hero mission, provided you kill every Black Arms soldier/gunship you can find.
Many parts of the stages Black Comet and The Last Way are identical to Final Haunt, with the former flooded with toxic liquid and the latter having some of its doors inaccessible requiring the use of Chaos Control.
When Sonic meets Shadow, he says "Well, Shadow, looks like we've reached the climax of this little game." but the subtitles read "Well, Shadow, looks like we've reached the climax of our little game."